[BioC] Long Time Series analysis

Maciej Jończyk mjonczyk at biol.uw.edu.pl
Wed Aug 18 10:38:51 CEST 2010

Dear Xiaokuan,

> Date: Wed, 11 Aug 2010 21:12:04 -0700 (PDT)

> From: Xiaokuan Wei <weixiaokuan at yahoo.com>

> To: bioconductor at stat.math.ethz.ch

> Subject: [BioC] Long Time Series analysis


> Dear List,


> I?was using?maSigPro for time series analysis of microarray.?I

> have about 12

> time points for a yeast data, and each time point only has two

> replicates. I am

> wondering if I can use quadratic model?to perform the analysis. If I

> used higher

> order model, will overfitting become a problem?

I've done analysis of time-course experiment with seven points, I
considered to use 3rd or 4th order polynomial. Eventually it turned out
that 3rd order is enought, 4th order gives nothing new.

I advise you to try with quadratic model, 3rd, 4th and maybe higer order
polynomial too and to look if it gives different results, if not lower
level polynomial is enought.


> I noticed that in?maSigPro tutorial, 4.4 mentioned "Long Time

> Series". But it

> has no detailed explaination. Does Ana or someone can share?some

> examples I can

> follow for such analysis?

I've asked for longer than mentioned 5 time points series and I've been
informed that in case of 7 time points I can use normal workflow.


> Any other packages I can use for a long time series analysis?

You can look in "packages" section at the Bioconductor website.

Hope it helps somehow.

> Your help will be greatly appreciated.


> Thanks again.


> Regards,

> Xiaokuan


Maciej Jończyk, MSc

Department of Plant Molecular Ecophysiology

Institute of Plant Experimental Biology

Faculty of Biology, University of Warsaw

02-096 Warszawa, Miecznikowa 1

NOCC, http://nocc.sourceforge.net

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